Yes, FIFA's six-plus-five rule was justified, because FIFA wanted players to represent their own nation in competition. It is sometimes frustrating to watch professional sporting events, knowing that none of the players are from the city or nation that they are playing for. Fans might have more pride in watching a sporting event knowing that the players are actually from the area.
The six-plus-five rule was a two-year experiment by FIFA to try to keep homegrown players on football clubs. After just two years, the rule was dropped. When finances and paychecks rule professional sports, FIFA tried to level the playing field unfairly. Players should be able to play where ever they want for whatever amount they want in whatever country they choose.